The paper is devoted to the assessment problems of the ecological costs management of the production in the project activity. The authors study the conditions of preparation and implementation of investment projects to eliminate accumulated environmental damage in the context of “green” economy. The technogenic deposits’ use approaches are considered for the purpose of the production costs optimization. The paper explains the necessity of building the fund liquidation (a fund for future generations) in the depletion of resource base of the enterprise. The proposed mechanism for the management of environmental costs in project activities can be used at the enterprises of Russia and Mongolia. For example, the Mongolian-Russian mining company “Erdenet” in Mongolia shows the direction to reduce costs and production costs through the implementation of measures for resource and energy efficiency, involving economic circulation of off-balance ores and tailings.